Mingchen Chen

The paper introduces Seq2Kd, a deep learning model predicting TF-DNA binding affinity using high-throughput Kd measurements, and provides a web portal for functional genomics and disease research.

This paper designs high-affinity protein binders using a computational framework combining flow matching and in silico maturation, achieving picomolar and nanomolar affinities without experimental screening.

AF3Score is a score-only adaptation of AlphaFold3 that evaluates biomolecular structures without iterative refinement, showing improved performance in binder screening and fold-switching protein analysis.

This paper introduces OpenAWSEM and Open3SPN2, GPU-accelerated coarse-grained simulation tools for proteins and DNA, enabling faster and more flexible modeling of biomolecular systems.